1,721,046 research outputs found
Sequence-specific termination by T7 RNA polymerase requires formation of paused conformation prior to the point of RNA release
No full textBackground: The sequence-specific, hairpin-independent termination signal for the bacteriophage RNA polymerases in Escherichia coli rrnB t1 terminator consists of two modules. The upstream module includes the conserved sequence and the downstream one is U-rich. Results: Elongation complexes of T7 RNA polymerase paused 2 bp before reaching the termination site at a 500 mum concentration of NTP. At 5-50 mum NTP, however, they paused and terminated there or resumed elongation beyond the termination site. Only at higher concentrations of NTP (500 mum), the pause complex proceeded slowly to and became incompetent at the termination site. At 4 bp or more before the termination site, the unprotected single-stranded region of transcription bubble shrank at the trailing edge to 4-5 bp from approximate to 10 bp, resulting from duplex formation of the conserved sequence. The pause and bubble collapse were not observed with an inactive mutant of the termination signal. Conclusion: Sequence-specific termination requires the slow elongation mode of paused conformation, working only at high concentrations of NTP for a few bp prior to the RNA release site. The collapse of bubble that was observed several base pairs before the termination site and/or the resulting duplex might subsequently lead to the paused conformation of T7 elongation complexes
Application of real-time DEVS to analysis of safety-critical embedded control systems: Railroad crossing control example
No full textThis article presents an application of the Discrete Event System Specification (DEVS) framework to the design and safety analysis of a real-time embedded control system, a railroad crossing control system. The authors employ an extension of the DEVS formalism, real-time DEVS (RT-DEVS), which has a sound semantics for the specification of real-time systems in a hierarchical modular fashion. The notion of a clock matrix for communicating RT-DEVS models is proposed, which represents a global time between the models. Based on the composition rules and the clock matrix, an algorithm for the generation of a timed reachability tree is developed that can be used for safety analysis at two phases: an untimed and timed analysis phase. A railroad crossing control example demonstrates that the proposed analysis for RT-DEVS models would be effective to verify the safety property of real-time control systems
Development of the dexterous manipulator and the force sensor for minimally invasive surgery
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Development of Flexible Surgical Manipulator for Natural Orifice Transluminal Endoscopic Surgery
No full textA real-time discrete event system specification formalism for seamless real-time software development
No full textWe present a time domain extension of the hierarchical and modular discrete event specification(DEVS) formalism. This extension is important for establishing a seamless real-time software development framework. Formalisms help describe a system unambiguously. If formal models are implemented without any consistent frameworks, however, it is hard to guarantee that there is no semantic gap between models and codes. Real-Time DEVS, named RTDEVS, is an extension of DEVS that can be characterized in three perspectives: the real time execution of models, the addition of time interval functions, and the activity specification for each state. After analyzing a system, the framework based on RTDEVS helps to expand each model of the system for executing in a real-time environment. In order to support the RTDEVS formalism, we propose abstract executive concepts based on the abstract simulator concepts of the DEVS formalism. Also, we implement an RTDEVS execution engine, named DEVS Executive, which runs on real-time Mach
DEVS framework for modelling, simulation, analysis, and design of hybrid systems
No full textWe make the case that Discrete Event System Specification (DEVS) is a universal formalism for discrete event dynamical systems (DEDS). DEVS offers an expressive framework for modelling, design, analysis and simulation of autonomous and hybrid systems. We review some known features of DEVS and its extensions. We then focus on the use of DEVS to formulate and synthesize supervisory level controllers
Development of FBG sensor system for Force-feedback in Minimally Invasive Robotic Surgery
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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